MicrobiomeAnalyst allows users to compute diversity based on either original OTUs or collapsing the data at different taxonomy levels. Note, in the later case, OTUs without taxa designation will be collapsed into a “Not_Assigned” category, which could be an arbitrary mix of OTUs from across different levels.
In some cases, OTUs without genus/species information are often more abundant and more representative of total diversity than are OTUs with genus/species names. Because of these issues, to understand the real diversity, it is recommended to first perform diversity analysis at OTU level before collapsing data by their taxonomy assignment.
When OTUs are well annotated or the selected taxonomy level includes the majority of the OTUs, it is biologically useful to perform diversity analysis at higher taxa levels for both data reductions and hypothesis generations.